Contacts of the strand formed by residues 454 - 458 (chain B) in PDB entry 1R9J
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 454 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B LEU* 5.8 0.4 - - + -
416B LEU* 4.2 2.8 - - - +
426B ILE* 5.0 7.0 - - + -
427B PRO 3.0 9.0 + - - +
428B PHE* 2.9 15.2 - - + +
429B GLY 2.9 25.3 + - - -
452B ARG* 5.2 4.7 - - + -
453B VAL* 1.3 81.4 - - - +
455B TYR* 1.3 65.8 + - - +
456B VAL* 4.7 0.2 - - + -
501B TRP* 3.7 28.0 - - + -
504B ALA* 3.4 40.8 - - + +
505B LEU* 4.0 15.9 - - + +
512B THR* 3.5 7.0 - - - +
514B LEU* 3.6 30.1 - - + -
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Residues in contact with TYR 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B MET* 5.9 0.4 - - + -
413B CYS* 3.6 38.4 + - + +
416B LEU* 4.2 14.1 - - + -
417B ASN* 4.6 1.7 + - - -
429B GLY 3.4 7.2 - - - +
436B ILE* 4.4 19.3 - - + -
442B ALA 4.5 1.2 + - - -
443B VAL* 3.6 28.5 + - + -
446B ALA* 3.4 16.6 - - - +
453B VAL* 3.3 30.2 - - + +
454B ILE* 1.3 74.0 - - - +
456B VAL* 1.3 59.8 + - - +
457B ALA 3.2 2.6 + - - +
486B LEU* 4.6 0.7 - - + -
511B PRO* 4.2 10.3 - - + -
512B THR 2.8 28.4 + - - +
513B VAL* 3.5 29.1 - - + +
514B LEU* 2.7 32.7 + - - +
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Residues in contact with VAL 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B SER* 4.0 8.3 - - - +
360B LEU* 5.2 0.2 - - + -
381B ASN* 4.5 2.4 - - - +
383B THR* 3.9 18.4 - - + -
428B PHE* 3.8 25.6 - - + -
429B GLY 2.9 10.9 + - - +
430B GLY* 3.2 23.5 - - - -
431B THR 3.2 6.6 + - - +
454B ILE* 4.7 0.2 - - + -
455B TYR* 1.3 70.9 - - - +
457B ALA* 1.3 58.5 + - - +
458B THR* 3.6 11.6 + - + +
501B TRP* 3.6 31.4 - - + -
514B LEU* 4.1 8.1 - - + -
516B LEU* 3.4 23.8 - - + -
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Residues in contact with ALA 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B THR* 3.3 7.9 - - - +
433B LEU* 3.6 38.9 - - + +
436B ILE* 4.3 11.0 - - + -
455B TYR 3.2 1.5 + - - +
456B VAL* 1.3 70.8 - - - +
458B THR* 1.3 59.9 + - - +
513B VAL* 4.2 11.4 - - + -
514B LEU 2.8 16.1 + - - +
515B CYS* 3.5 2.1 - - - -
516B LEU* 2.8 28.7 + - - +
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Residues in contact with THR 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ARG* 4.0 17.3 - - + -
381B ASN* 2.6 57.9 + - + +
431B THR 3.1 4.2 + - - -
432B PHE* 3.4 2.6 - - - -
433B LEU 2.8 24.9 + - - -
456B VAL* 4.2 4.5 - - + -
457B ALA* 1.3 72.1 - - - +
459B HIS* 1.3 82.6 + - - +
460B ASP 3.3 0.6 + - - -
516B LEU* 3.2 27.6 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il